2MXJ | pdb_00002mxj

Structural features of a 3' splice site influenza A: 11-nt hairpin

• PDB DOI: https://doi.org/10.2210/pdb2MXJ/pdb
• BMRB: 25414
• NAKB: 2MXJ

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2015-01-06 Released: 2015-05-06 
• Deposition Author(s): Turner, D.H., Kennedy, S.D., Chen, J.L.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: lowest NOE restraint violation energy 

Literature

Structural features of a 3' splice site in influenza a.

Chen, J.L., Kennedy, S.D., Turner, D.H.

(2015) Biochemistry 54: 3269-3285

• PubMed: 25909229 
• DOI: https://doi.org/10.1021/acs.biochem.5b00012
• Primary Citation Related Structures: 
  2MXJ, 2MXK, 2MXL


• PubMed Abstract: 
  

  Influenza A is an RNA virus with a genome of eight negative sense segments. Segment 7 mRNA contains a 3' splice site for alternative splicing to encode the essential M2 protein. On the basis of sequence alignment and chemical mapping experiments, the secondary structure surrounding the 3' splice site has an internal loop, adenine bulge, and hairpin loop when it is in the hairpin conformation that exposes the 3' splice site. We report structural features of a three-dimensional model of the hairpin derived from nuclear magnetic resonance spectra and simulated annealing with restrained molecular dynamics. Additional insight was provided by modeling based on (1)H chemical shifts. The internal loop containing the 3' splice site has a dynamic guanosine and a stable imino (cis Watson-Crick/Watson-Crick) GA pair. The adenine bulge also appears to be dynamic with the A either stacked in the stem or forming a base triple with a Watson-Crick GC pair. The hairpin loop is a GAAA tetraloop closed by an AC pair.

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Organizational Affiliation: 
• †Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.
‡Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States.
§Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.55 kDa 
• Atom Count: 236 
• Modeled Residue Count: 11 
• Deposited Residue Count: 11 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA_(11-MER)	A	11	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: lowest NOE restraint violation energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Turner, D.H., Kennedy, S.D., Chen, J.L.

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2015-06-17
  Changes: Database references, Source and taxonomy
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references